layman question about TDC

[bugsiegel]

I reading Flathead Facts and on page 20 and 21 the book describes inserting a wire between the head and the piston to feel the piston reach its highest point, which will be marked on a pulley. then it says to rotate the engine the opposite direction and make a second mark which will be on a different location and also marked. The difference between is TDC.
I'm going to say the obvoius so that it's covered in the question. All the above is done on the combustion stroke.
So my question is why don't the two marks align with each other? is the difference the play in the push rod to the piston in relation to the direction of rotation?
and then if different marks are achieved in different directions shouldn't the more important mark be the one that represents the direction of the engine while running?
Go easy on me , my engine experience is a hand full of two stroke engines.
I do understand the basics of two strokes vrs four strokes

Thank in advance
Paul